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Personally, I tend to do this outside of Qtractor itself. In short. the pseudo work flow looks like this...(unix knowledge assumed)

cp -R path/to/old/project/dir path/to/new/project/dir
vi path/to/new/project/dir/$file.qtr

Now update the path between the <directory> and </directory> nodes accordingly as this is where the .mid and any .wav files are expected to exist.

This approach is far more predictable IMHO and also assists with project renames.